South Korean striker Son scored a hat-trick in the 6-0 win as the North London club registered a Wembley semi-final spot at the expense of their local rivals.
When asked about the alleged racist chants and the subsequent investigation, Millwall boss Neil Harris said: "What I will say is me personally - and the club - we won't condone that.
"We came here in the right spirit, to enjoy an FA Cup quarter-final, so if that's proven to have been to the detriment to the competition then I'm sure it will be left to the authorities. We just want people to enjoy the game.
"Of course it's a shame, for both of us - Mauricio wants to be talking about his team's quality.
"The focus comes away from what we've achieved in the competition. It's wrong in society and it's wrong in football."